ENT MERFISH Report
1. Overview
1.1 Sample Information
A brief sample information is generated from the submission table for the following analysis.
| Expt | Sample | Index | Case_Number | Sex | Age | HPV | Sample_Region | Genotype | Group | Region | DataPath | Clinic.comment |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | NT28530x2 | NT28530 | 1 | M | 52 | Negative | Left posterior BOT | NT | Normal | region_NT28530x2 | Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 | Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K. |
| 1 | TT28519x1 | TT28519 | 1 | M | 52 | Negative | Left posterior BOT | TT | Tumor | region_TT28519x1 | Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 | Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K. |
| 1 | TT28519x2 | TT28519_dup | 1 | M | 52 | Negative | Left posterior BOT | TT | Tumor | region_TT28519x2 | Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 | Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K. |
| 1 | NT28530x1 | NT28530_dup | 1 | M | 52 | Negative | Left posterior BOT | NT | Normal | region_NT28530x1 | Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 | Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K. |
1.2 MERSCOPE Data Quality Summary
The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.
Generally, log10 transcript count > 4.0 in most area can be considered as a good quality standard for human tissue.
Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.
1.2.1 NT28530x2(Normal)
1.2.2 TT28519x1(Tumor)
1.2.3 TT28519x2(Tumor)
1.2.4 NT28530x1(Normal)
1.3 Transcript Mis-Match on FOV Boundary
Due to issues with the Vizgen software, transcript alignment is incorrect during decoding, leading to misalignment problems at the field of view (FOV) boundary.
Vizgen has solved this issue by temporarily updating the decoding software to an unpublished beta version.
However, this update also made the “vzg” file being upgraded to “vzg2”. Current Vizgen Visualizer cannot recognize the new data format, which made Visualizer unusable for this dataset.
1.4 Autofluorescent issue
Autofluorescence is a major problem limiting the sensitivity of the detection of the fluorescence specifically derived from the applied dye or probe. As we can find it on DAPI imaging, there are many over-bright region.
Autofluorescence may occur due to the incomplete clearance of the tissue. Because of the presence of autofluorescence, the decoding would be confounded and the results in these cells would be artifacts.
As Dr. Tan highly recommends, we removed the portion of cell with autofluorescent issue, for better accuracy.
NT28530_DAPI_Imaging
NT28530_DAPI_Imaging_small
NT28530_dup_DAPI_Imaging
NT28530_dup_DAPI_Imaging_small